Question

gatk4 download issue

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12 months ago

bestone ▴ 30

Hello guys, I try to download gatk4 to my Mac but I couldn't download it. it gives this error:

conda env create -n gatk4 -f gatkcondaenv.yml
Collecting package metadata (repodata.json): failed

UnavailableInvalidChannel: HTTP 404 NOT FOUND for channel biconda <https://conda.anaconda.org/biconda>

The channel is not accessible or is invalid.

You will need to adjust your conda configuration to proceed.
Use `conda config --show channels` to view your configuration's current state,
and use `conda config --show-sources` to view config file locations

Could you pls help me with this issue?

gatk4 • 1.2k views

ADD COMMENT • link 12 months ago by bestone ▴ 30

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bioconda, not biconda

ADD REPLY • link 12 months ago by Shred ★ 1.4k

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hello thank you for your reply. I run this code:

conda install -c bioconda gatk
Retrieving notices: ...working... done
Collecting package metadata (current_repodata.json): failed

UnavailableInvalidChannel: HTTP 404 NOT FOUND for channel biconda <https://conda.anaconda.org/biconda>

The channel is not accessible or is invalid.

You will need to adjust your conda configuration to proceed.
Use `conda config --show channels` to view your configuration's current state,
and use `conda config --show-sources` to view config file locations.

I am still getting this error. I couldn't figure it out

ADD REPLY • link updated 12 months ago by GenoMax 141k • written 12 months ago by bestone ▴ 30

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Have you tried to run the two commands conda is suggesting. See what you get with conda config --show channels. Looks like the word biconda may still be in your .condarc file that will need to be taken out.

ADD REPLY • link 12 months ago by GenoMax 141k

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When I run gatk on terminal it gives this code is it work?

/Users/uguremre/opt/anaconda3/bin/gatk:80: SyntaxWarning: "is" with a literal. Did you mean "=="?
  if len(args) is 0 or (len(args) is 1 and (args[0] == "--help" or args[0] == "-h")):
/Users/uguremre/opt/anaconda3/bin/gatk:80: SyntaxWarning: "is" with a literal. Did you mean "=="?
  if len(args) is 0 or (len(args) is 1 and (args[0] == "--help" or args[0] == "-h")):
/Users/uguremre/opt/anaconda3/bin/gatk:117: SyntaxWarning: "is" with a literal. Did you mean "=="?
  if len(args) is 1 and args[0] == "--list":
/Users/uguremre/opt/anaconda3/bin/gatk:301: SyntaxWarning: "is" with a literal. Did you mean "=="?
  if call(["gsutil", "-q", "stat", gcsjar]) is 0:
/Users/uguremre/opt/anaconda3/bin/gatk:305: SyntaxWarning: "is" with a literal. Did you mean "=="?
  if call(["gsutil", "cp", jar, gcsjar]) is 0:
/Users/uguremre/opt/anaconda3/bin/gatk:458: SyntaxWarning: "is not" with a literal. Did you mean "!="?
  if not len(properties) is 0:
/Users/uguremre/opt/anaconda3/bin/gatk:462: SyntaxWarning: "is not" with a literal. Did you mean "!="?
  if not len(filesToAdd) is 0:

 Usage template for all tools (uses --spark-runner LOCAL when used with a Spark tool)
    gatk AnyTool toolArgs

 Usage template for Spark tools (will NOT work on non-Spark tools)
    gatk SparkTool toolArgs  [ -- --spark-runner <LOCAL | SPARK | GCS> sparkArgs ]

 Getting help
    gatk --list       Print the list of available tools

    gatk Tool --help  Print help on a particular tool

 Configuration File Specification
     --gatk-config-file                PATH/TO/GATK/PROPERTIES/FILE

 gatk forwards commands to GATK and adds some sugar for submitting spark jobs

   --spark-runner <target>    controls how spark tools are run
     valid targets are:
     LOCAL:      run using the in-memory spark runner
     SPARK:      run using spark-submit on an existing cluster 
                 --spark-master must be specified
                 --spark-submit-command may be specified to control the Spark submit command
                 arguments to spark-submit may optionally be specified after -- 
     GCS:        run using Google cloud dataproc
                 commands after the -- will be passed to dataproc
                 --cluster <your-cluster> must be specified after the --
                 spark properties and some common spark-submit parameters will be translated 
                 to dataproc equivalents

   --dry-run      may be specified to output the generated command line without running it
   --java-options 'OPTION1[ OPTION2=Y ... ]'   optional - pass the given string of options to the

ADD REPLY • link updated 12 months ago by GenoMax 141k • written 12 months ago by bestone ▴ 30

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Yes it is working. You will need to run something like gatk --help to actually see useful in-line help,

ADD REPLY • link 12 months ago by GenoMax 141k

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Thank you so much for helping. I tried to run. I got this error. Could you pls help me with that too:( I am sorry i asked so many questions but I have to figure it out.

gatk --java-options "-Xmx4g" HaplotypeCaller \ -R one_chromosome.fasta \ -I input.bam \ -O output.vcf Using GATK jar /Users/uguremre/opt/anaconda3/envs/gatk/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx4g -jar /Users/uguremre/opt/anaconda3/envs/gatk/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar HaplotypeCaller -R one_chromosome.fasta -I input.bam -O output.vcf 19:10:35.064 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Users/uguremre/opt/anaconda3/envs/gatk/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib 19:10:35.639 INFO HaplotypeCaller - ------------------------------------------------------------ 19:10:35.643 INFO HaplotypeCaller - The Genome Analysis Toolkit (GATK) v4.4.0.0 19:10:35.643 INFO HaplotypeCaller - For support and documentation go to https://software.broadinstitute.org/gatk/ 19:10:35.643 INFO HaplotypeCaller - Executing as uguremre@Macs-MacBook-Pro.local on Mac OS X v13.2.1 x86_64 19:10:35.643 INFO HaplotypeCaller - Java runtime: OpenJDK 64-Bit Server VM v17.0.3+7-LTS 19:10:35.643 INFO HaplotypeCaller - Start Date/Time: April 14, 2023 at 7:10:35 PM TRT 19:10:35.644 INFO HaplotypeCaller - ------------------------------------------------------------ 19:10:35.644 INFO HaplotypeCaller - ------------------------------------------------------------ 19:10:35.644 INFO HaplotypeCaller - HTSJDK Version: 3.0.5 19:10:35.644 INFO HaplotypeCaller - Picard Version: 3.0.0 19:10:35.645 INFO HaplotypeCaller - Built for Spark Version: 3.3.1 19:10:35.645 INFO HaplotypeCaller - HTSJDK Defaults.COMPRESSION_LEVEL : 2 19:10:35.645 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 19:10:35.645 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 19:10:35.646 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 19:10:35.646 INFO HaplotypeCaller - Deflater: IntelDeflater 19:10:35.646 INFO HaplotypeCaller - Inflater: IntelInflater 19:10:35.647 INFO HaplotypeCaller - GCS max retries/reopens: 20 19:10:35.647 INFO HaplotypeCaller - Requester pays: disabled 19:10:35.647 INFO HaplotypeCaller - Initializing engine 19:10:35.651 INFO HaplotypeCaller - Shutting down engine [April 14, 2023 at 7:10:35 PM TRT] org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=104857600

A USER ERROR has occurred: Fasta index file file:///Users/uguremre/gatk-4.4.0.0/one_chromosome.fasta.fai for reference file:///Users/uguremre/gatk-4.4.0.0/one_chromosome.fasta does not exist. Please see http://gatkforums.broadinstitute.org/discussion/1601/how-can-i-prepare-a-fasta-file-to-use-as-reference for help creating it.

Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace.

ADD REPLY • link 12 months ago by bestone ▴ 30